Locus 3477

Sequence ID	2R_DroMel_CAF1
Location	11,684,527 – 11,684,630
Length	103
Max. P	0.842729

overview

Window 3

Location	11,684,527 – 11,684,630
Length	103
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	81.42
Mean single sequence MFE	-40.67
Consensus MFE	-24.34
Energy contribution	-26.98
Covariance contribution	2.64
Combinations/Pair	1.16
Mean z-score	-2.59
Structure conservation index	0.60
SVM decision value	0.76
SVM RNA-class probability	0.842729
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11684527 103 + 20766785
UGGUCAGUUGGAAUCCUCUGAGCUGUCACUGUAGGCAGCCAAGAGGGAAAGUCCAGCUGGAGCGGCAGCUGGCUGAUUUGUAGCUUUAGUUUCCGCUGGUGCA
...(((((((((.((((((..((((((......))))))..))))))....)))))))))(((((.(((((((((.....)))))..)))).)))))...... ( -47.10)
>DroPse_CAF1 19471 100 + 1
GUGUCAGGUGGAAUCCUCUGAGCUAUCGCUAUAGGCGGCUAGAAGGGAUAGACCCGCUG---CUGGAGCUGGGGUCUUUGAAACUUCAGCUGCCUUUGGAAUA
...(((((.((...))))))).......(((.((((((((.((((....((((((.(.(---(....)).)))))))......)))))))))))).))).... ( -38.40)
>DroSec_CAF1 24707 103 + 1
UGGUCAGUUGGAAUCCUCUGAGCUGUCACUGUAGGCAGCCAAAAGGGAAAGUCCAGCUGGAGCGGCAGCUGGCUGAUUUGUAGCUUUAGUUUCCGGUGGAGCA
...(((((((((.((((.((.((((((......))))))))...))))...)))))))))(.(((.(((((((((.....)))))..)))).))).)...... ( -38.00)
>DroSim_CAF1 20608 103 + 1
UGGUCAGUUGGAAUCCUCUGAGCUGUCACUGUAGGCAGCCAAAAGGGAAAGUCCAGCUGGAGCGGCAGCUGGCUGAUUUGUAGCUUUAGUUUCCGGUGGAGCA
...(((((((((.((((.((.((((((......))))))))...))))...)))))))))(.(((.(((((((((.....)))))..)))).))).)...... ( -38.00)
>DroEre_CAF1 20671 103 + 1
UGGUCAGUUGGAAUCCUCUGAGCUGUCACUGUAGGCAGCCAAGAGGGAUAGUCCAACUGGAGCGGCAGCUGGCUGAUUUGUAGCUUUAGUUUCCGGUGGUGCG
...(((((((((.((((((..((((((......))))))..))))))....)))))))))(.(((.(((((((((.....)))))..)))).))).)...... ( -42.60)
>DroAna_CAF1 22684 103 + 1
UGGUCAGUUGGAAUCUUCGGAACUGUCGCUGUAAGCAGCCAAAAGUGAUAGCCCAGCUGGCGCGGAAGAUGCAGGAGUAGGGGCUUUUGGUUCUGCUGCCGUA
..(((((((((..((....)).((((((((.............)))))))).)))))))))((((.....((((((.((((....)))).))))))..)))). ( -39.92)
>consensus
UGGUCAGUUGGAAUCCUCUGAGCUGUCACUGUAGGCAGCCAAAAGGGAAAGUCCAGCUGGAGCGGCAGCUGGCUGAUUUGUAGCUUUAGUUUCCGGUGGAGCA
...(((((((((.((((....((((((......)))))).....))))...)))))))))..(((.(((((((((.....)))))..)))).)))........ (-24.34 = -26.98 +   2.64)

alignment

secondary structure

dotplot

Window 4

Location	11,684,527 – 11,684,630
Length	103
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	81.42
Mean single sequence MFE	-29.85
Consensus MFE	-20.32
Energy contribution	-21.43
Covariance contribution	1.12
Combinations/Pair	1.27
Mean z-score	-2.16
Structure conservation index	0.68
SVM decision value	0.71
SVM RNA-class probability	0.829178
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11684527 103 - 20766785
UGCACCAGCGGAAACUAAAGCUACAAAUCAGCCAGCUGCCGCUCCAGCUGGACUUUCCCUCUUGGCUGCCUACAGUGACAGCUCAGAGGAUUCCAACUGACCA
.....(((.((((................(((((((((......))))))).))...(((((.(((((.(......).))))).))))).))))..))).... ( -33.40)
>DroPse_CAF1 19471 100 - 1
UAUUCCAAAGGCAGCUGAAGUUUCAAAGACCCCAGCUCCAG---CAGCGGGUCUAUCCCUUCUAGCCGCCUAUAGCGAUAGCUCAGAGGAUUCCACCUGACAC
...(((..((((.(((((((......(((((((.((....)---).).))))))....)))).))).))))..(((....)))....)))............. ( -30.30)
>DroSec_CAF1 24707 103 - 1
UGCUCCACCGGAAACUAAAGCUACAAAUCAGCCAGCUGCCGCUCCAGCUGGACUUUCCCUUUUGGCUGCCUACAGUGACAGCUCAGAGGAUUCCAACUGACCA
.(((.....(....)...)))......(((((((((((......)))))))......(((((.(((((.(......).))))).))))).......))))... ( -30.30)
>DroSim_CAF1 20608 103 - 1
UGCUCCACCGGAAACUAAAGCUACAAAUCAGCCAGCUGCCGCUCCAGCUGGACUUUCCCUUUUGGCUGCCUACAGUGACAGCUCAGAGGAUUCCAACUGACCA
.(((.....(....)...)))......(((((((((((......)))))))......(((((.(((((.(......).))))).))))).......))))... ( -30.30)
>DroEre_CAF1 20671 103 - 1
CGCACCACCGGAAACUAAAGCUACAAAUCAGCCAGCUGCCGCUCCAGUUGGACUAUCCCUCUUGGCUGCCUACAGUGACAGCUCAGAGGAUUCCAACUGACCA
.((......(....)...((((...........))))...))..((((((((..((((.(((.(((((.(......).))))).))))))))))))))).... ( -31.90)
>DroAna_CAF1 22684 103 - 1
UACGGCAGCAGAACCAAAAGCCCCUACUCCUGCAUCUUCCGCGCCAGCUGGGCUAUCACUUUUGGCUGCUUACAGCGACAGUUCCGAAGAUUCCAACUGACCA
...((.(((((..(((((((.(((..((..(((.......)))..))..)))......))))))))))))........(((((..((....)).))))).)). ( -22.90)
>consensus
UGCUCCACCGGAAACUAAAGCUACAAAUCAGCCAGCUGCCGCUCCAGCUGGACUAUCCCUUUUGGCUGCCUACAGUGACAGCUCAGAGGAUUCCAACUGACCA
.........((((..................(((((((......)))))))......(((((.(((((.(......).))))).))))).))))......... (-20.32 = -21.43 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:33 2006